is chantry evil?
well. it's a political structure and institute of faith. take it as you want.
however i find position of the Chantry about the mages very stupid. Chantry had direct control over mages and their breeding inside the Circles. So they could run eugenics programs on a basis of the Circles. But they didn't. Chantry also were separating mage parents with their mage childs, which is dumb as well. Not because of some feelings or some other crap, but simply because such behavior do not inspire loyalty. You can't ingrain loyalty to a child as well, because people around this child will have different take on the worlds and things around them, so there is no chance on running indoctrination program from birth.
So basically Chantry were not using advantages and leverages they had on mages, which is stupid. Just in few generations attitude of mages towards circles would had been changed. But nope, let us be dumb priests instead.
Same goes for city elves as well to be honest.
So you can considered politics of the Chantry as humane approach or as stupid approach.